# HG changeset patch
# User devteam
# Date 1411569780 14400
# Node ID 39472bc02d8d7de49d040d75c443b6fe9ec29e11

Uploaded initial tool tarball.

diff -r 000000000000 -r 39472bc02d8d samtools_calmd.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_calmd.xml	Wed Sep 24 10:43:00 2014 -0400
@@ -0,0 +1,110 @@
+<tool id="samtools_calmd" name="Recalculate" version="1.0.0">
+    <description>MD/NM tags and '=' bases</description>
+    <requirements>
+        <requirement type="package" version="1.0">samtools</requirement>
+    </requirements>
+    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    <command><![CDATA[
+        #if str( $reference_source.reference_source_selector ) == "history":
+            #set ref_fa = 'ref.fa'
+            ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa &&
+        #else:
+            #set ref_fa = str( $reference_source.ref_fasta.fields.path )
+        #end if
+        samtools calmd
+        #if str($option_set.option_sets) == 'advanced':
+            $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq
+        #end if
+        -b "$input_bam" "$ref_fa" > "$calmd_output" ]]>
+    </command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <inputs>
+        <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" />
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference FASTA">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="ref_fasta" type="select" label="Using reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" column="value" key="dbkey" ref="input_bam" />
+                        <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
+            </when>
+        </conditional>
+        <conditional name="option_set">
+            <param name="option_sets" type="select" label="Options">
+                <option value="default">Use defaults</option>
+                <option value="advanced">Advanced options</option>
+            </param>
+            <when value="default" />
+            <when value="advanced">
+                <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" />
+                <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" />
+                <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" />
+                <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="option_sets" value="default" /> 
+            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
+            <param name="reference_source|reference_source_selector" value="history" />
+            <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
+            <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
+        </test>
+        <!-- Using the test-data-repo's phiX.fa should produce the same output. -->
+        <test>
+            <param name="option_sets" value="default" /> 
+            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
+            <param name="reference_source|reference_source_selector" value="cached" />
+            <param name="ref_fasta" value="phiX" />
+            <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
+        </test>
+        <test>
+            <param name="option_sets" value="advanced" /> 
+            <param name="change_identical" value="true" />
+            <param name="extended_baq" value="true" />
+            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
+            <param name="reference_source|reference_source_selector" value="history" />
+            <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" />
+            <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
+        </test>
+        <!-- Using the test-data-repo's phiX.fa should, as before, produce the same output. -->
+        <test>
+            <param name="option_sets" value="advanced" /> 
+            <param name="change_identical" value="true" />
+            <param name="extended_baq" value="true" />
+            <param name="input_bam" value="phiX.bam" dbkey="phiX" />
+            <param name="reference_source|reference_source_selector" value="cached" />
+            <param name="ref_fasta" value="phiX" />
+            <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. 
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+        </help>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 39472bc02d8d test-data/phiX.bam
Binary file test-data/phiX.bam has changed
diff -r 000000000000 -r 39472bc02d8d test-data/phiX.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta	Wed Sep 24 10:43:00 2014 -0400
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
diff -r 000000000000 -r 39472bc02d8d test-data/samtools_calmd_out_1.bam
Binary file test-data/samtools_calmd_out_1.bam has changed
diff -r 000000000000 -r 39472bc02d8d test-data/samtools_calmd_out_2.bam
Binary file test-data/samtools_calmd_out_2.bam has changed
diff -r 000000000000 -r 39472bc02d8d tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Wed Sep 24 10:43:00 2014 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r 39472bc02d8d tool-data/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample	Wed Sep 24 10:43:00 2014 -0400
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tables>
+    <table comment_char="#" name="fasta_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" />
+    <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table>
+
+<table comment_char="#" name="fasta_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" />
+    <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table>
+
+<table comment_char="#" name="fasta_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" />
+    <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table>
+
+<table comment_char="#" name="fasta_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" />
+    <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table>
+</tables>
\ No newline at end of file
diff -r 000000000000 -r 39472bc02d8d tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Sep 24 10:43:00 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="samtools" version="1.0">
+	<repository changeset_revision="da217d52e81c" name="package_samtools_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>